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Clifford Stoll, the author, managed some computers at Lawrence Berkeley National Laboratory in California. One day, in August 1986, his supervisor, Dave Cleveland, asked him to resolve a US$0.75 accounting error in the computer usage accounts. He traced the error to an unauthorized user who had apparently used up 9 seconds of computer time and not paid for it, and eventually realized that the unauthorized user was a hacker who had acquired root access to the LBNL system by exploiting a vulnerability in the movemail function of the original GNU Emacs.

Over the next ten months, Stoll spent a great deal of time and effort tracing the hacker's origin. He saw that the hacker was using a 1200 baud connection and realized that the intrusion was coming through a telephone modem connection. Stoll's colleagues, Paul Murray and Lloyd Bellknap, helped with the phone lines. Over the course of a long weekend he rounded up fifty terminals, mostly by "borrowing" them from the desks of co-workers away for the weekend, and teleprinters and physically attached them to the fifty incoming phone lines. When the hacker dialed in that weekend, Stoll located the phone line, which was coming from the Tymnet routing service. With the help of Tymnet, he eventually tracked the intrusion to a call center at MITRE, a defense contractor in McLean, Virginia.

After returning his "borrowed" terminals, Stoll left a teleprinter attached to the intrusion line in order to see and record everything the hacker did. He watched as the hacker sought, and sometimes gained unauthorized access to military bases around the United States, looking for files that contained words such as "nuclear" or "SDI". The hacker also copied password files (in order to make dictionary attacks) and set up Trojan horses to find passwords. Stoll was amazed that on many of these high-security sites the hacker could easily guess passwords, since many system administrators never bothered to change the passwords from their factory defaults. Even on military bases, the hacker was sometimes able to log in as "guest" with no password.

Over the course of this investigation, Stoll contacted various agents at the FBI, CIA, NSA, and Air ForceOSI. Since this was almost the first documented case of a computer break-in — Stoll seems to have been the first to keep a daily logbook of the hacker's activities — there was some confusion as to jurisdiction and a general reluctance to share information.

Studying his log book, Stoll saw that the hacker was familiar with VMS, as well as AT&T Unix. He also noted that the hacker tended to be active around the middle of the day, Pacific time. Stoll hypothesized that since modem bills are cheaper at night, and most people have school or a day job and would only have a lot of free time for hacking at night, the hacker was in a time zone some distance to the east.

With the help of Tymnet and various agents from various agencies, Stoll eventually found that the intrusion was coming from West Germany via satellite. The Deutsche Bundespost, the German post office, also had authority over the phone system, and they traced the calls to a university in Bremen. In order to entice the hacker to reveal himself, Stoll set up an elaborate hoax — known today as a honeypot — inventing a fictitious department at LBL that had supposedly been newly formed because of an SDI contract. He knew the hacker was mainly interested in SDI, so he filled the "SDInet" account (operated by the imaginary secretary Barbara Sherwin) with large files full of impressive-sounding bureaucratese. The ploy worked, and the Deutsche Bundespost finally located the hacker at his home in Hanover. The hacker's name was Markus Hess, and he had been engaged for some years in selling the results of his hacking to the SovietKGB. There was ancillary proof of this when a Hungarianspy contacted the fictitious SDInet at LBL by mail, based on information he could only have obtained through Hess: Apparently this was the KGB's method of double-checking to see if Hess was just making up the information he was selling them.

Stoll later flew to Germany to testify at the trial of Hess and a confederate.

The number sequence mentioned in Chapter 48 has become a popular math puzzle, known as the Cuckoo's Egg, the Morris Number Sequence, or the look-and-say sequence.

In the summer of 2000 the name "Cuckoo's Egg" was used to describe a file sharing hack attempt that substituted white noise or sound effects files for legitimate song files on Napster and other networks.[3]

These events are referenced in Cory Doctorow's speculative fiction short story "The Things that Make Me Weak and Strange Get Engineered Away", as "(a) sysadmin who’d tracked a $0.75 billing anomaly back to foreign spy-ring that was using his systems to hack his military".[4]